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There aren't any fixed nature (Careful) encounters from Generation 3.

Encounter objects are templates, not actual PKM files. When you view an encounter object, PKHeX creates a new PKM from the template and puts it in the editor tabs. Recent commits since the last release allow for letting PKHeX use the current tabs values as a criteria when creating a PKM from an encounter object. If using the latest release, you can just repeatedly view an encounter until it meets your satisfaction, or use other tools to create a sufficiently valid PIDIV for manual editing.